I have used galaxy server GATK4 Mutect2 in Tumor only mode. THe output VCF has a warning showing that please run FilterMUtectCalls to remove false positive. but i didnot findd this tool on galaxy server. and my output vcf from mutect2 donot conatin quality score. please tell me how to fix these 2 problems.
Welcome, @wafa_khan
That message is from the underlying tool, and is referring to other tools in the GATK pipeline. Those are not hosted at public Galaxy servers as far as I know (and not at any of the UseGalaxy servers for certain).
I’m not sure if I understand, would you please explain more about this?
Is the VCF output dataset’s content the header only, with no data lines? That can indicate some data input problem, like a reference genome mismatch, or maybe there were really not any variants called with the current parameters.
If you are interested, we have alternative methods, and perhaps supplementary methods tools, described in the GTN. Variant Analysis / Tutorial List. This tutorial goes over the specific steps for a pair of samples, but you could just skip the steps for the comparison if you just have one. Hands-on: Identification of somatic and germline variants from tumor and normal sample pairs / Identification of somatic and germline variants from tumor and normal sample pairs / Variant Analysis
There are also many many ways to parse, filter and adjust VCF files in Galaxy outside of any tutorials. One simple but common choice is VCFfilter. Maybe you can determine how the GATK tool referenced is designed to filter the VCF (which attributes, what thresholds), then use alternative tools to perform the same manipulation?
We can help with troubleshooting reference data problems if you’d like some feedback about that part. See the banner for how to quickly share your work.
Hope this helps, and we can follow up more. 